DGRPool

GWAS results were computed on dm3 genome.

If you want to make an independent analysis with DGRP2 or PLINK2, you can find here prepared input files for this phenotype: DGRP2 results PLINK2 results

Full results

Phenotype distribution and association to known covariates

Shapiro-Wilk test of normality (p-value=3.184e^-1)
Null hypothesis is not rejected (p>0.05).
Interpretation: NORMAL distribution of this phenotype

We tested for association of this phenotype with 6 known covariates Huang et al., 2014 using both ANOVA and Kruskal-Wallis association tests.

ANOVA test
No significant result.

Kruskal-Wallis test
No significant result.

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

1738 significant hits at p-value < 0.001. The 1000 top results are displayed in the table below.

We performed a gene enrichment calculation (Fisher's exact test) of all GWAS-associated genes at p < 0.001. Genesets were taken from two database: the Gene Ontology (GO) and the FlyBase phenotypes. GO enrichment FlyBase phenotype enrichment

Variant impact HIGH MODERATE LOW MODIFIER

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Chromosome	Position	ID	Reference	Variant	p-value	FDR_BH	Transcript annotation	Binding site annotation
2R	9188938	2R_9188938_SNP [dm3] 2R_13301433_SNP [dm6]	C	T	4.898e^-7	0.917	SYNONYMOUS_CODING CG17047
2R	16664008	2R_16664008_SNP [dm3] 2R_20776503_SNP [dm6]	G	C	1.253e^-6	0.917	UPSTREAM CG43709 DOWNSTREAM CG43710 INTERGENIC
3L	6385138	3L_6385138_SNP [dm3] 3L_6392038_SNP [dm6]	G	A	1.467e^-6	0.917	INTERGENIC
2R	13445244	2R_13445244_SNP [dm3] 2R_17557739_SNP [dm6]	T	C	1.996e^-6	0.935	INTRON Klp54D
3R	11717240	3R_11717240_SNP [dm3] 3R_15891518_SNP [dm6]	A	G	3.269e^-6	0.985	INTRON CG14877
2R	18619246	2R_18619246_SNP [dm3] 2R_22731741_SNP [dm6]	T	C	3.877e^-6	0.985	SYNONYMOUS_CODING jbug	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
2L	9663804	2L_9663804_SNP [dm3] 2L_9663804_SNP [dm6]	T	A	6.821e^-6	0.985	INTERGENIC
2R	9180034	2R_9180034_SNP [dm3] 2R_13292529_SNP [dm6]	G	A	8.410e^-6	0.985	INTRON Dh31-R
3L	17190234	3L_17190234_DEL [dm3] 3L_17197134_DEL [dm6]	TATCT	T	8.493e^-6	0.985	INTRON Rbp6
X	9364184	X_9364184_SNP [dm3] X_9470151_SNP [dm6]	C	T	8.651e^-6	0.985	INTRON mgl
2L	2771103	2L_2771103_SNP [dm3] 2L_2771103_SNP [dm6]	C	T	1.045e^-5	0.985	SYNONYMOUS_CODING CG15399 DOWNSTREAM CG2862	TF binding site mE1_TFBS_eve mE1_TFBS_sens
X	16639487	X_16639487_SNP [dm3] X_16745454_SNP [dm6]	G	A	1.047e^-5	0.985	INTRON CG9634
3L	1832557	3L_1832557_SNP [dm3] 3L_1832557_SNP [dm6]	T	G	1.053e^-5	0.985	UPSTREAM Cpr62Ba DOWNSTREAM Cpr62Bb INTERGENIC
2R	9179910	2R_9179910_SNP [dm3] 2R_13292405_SNP [dm6]	T	C	1.135e^-5	0.985	INTRON Dh31-R
2R	19199701	2R_19199701_SNP [dm3] 2R_23312178_SNP [dm6]	C	T	1.179e^-5	0.985	DOWNSTREAM HP1Lcsd INTERGENIC	TF binding site mE1_TFBS_inv
X	7257505	X_7257505_SNP [dm3] X_7363472_SNP [dm6]	C	A	1.191e^-5	0.985	INTRON CG1677 & 1 other
2L	4104267	2L_4104267_SNP [dm3] 2L_4104267_SNP [dm6]	A	C	1.212e^-5	0.985	INTRON ed
X	16639512	X_16639512_SNP [dm3] X_16745479_SNP [dm6]	A	T	1.236e^-5	0.985	INTRON CG9634
2L	4104289	2L_4104289_SNP [dm3] 2L_4104289_SNP [dm6]	T	A	1.402e^-5	0.985	INTRON ed
2R	9189975	2R_9189975_SNP [dm3] 2R_13302470_SNP [dm6]	T	G	1.434e^-5	0.985	DOWNSTREAM CG17047 INTERGENIC
2L	13042700	2L_13042700_SNP [dm3] 2L_13042700_SNP [dm6]	C	G	1.695e^-5	0.985	INTRON CG9932
3R	19462264	3R_19462264_SNP [dm3] 3R_23636542_SNP [dm6]	G	A	1.788e^-5	0.985	INTRON CG31145
3L	20876088	3L_20876088_SNP [dm3] 3L_20882988_SNP [dm6]	G	A	1.825e^-5	0.985	INTRON CG32432
3L	17185700	3L_17185700_SNP [dm3] 3L_17192600_SNP [dm6]	C	T	1.844e^-5	0.985	INTRON Rbp6
3L	20868545	3L_20868545_SNP [dm3] 3L_20875445_SNP [dm6]	A	T	1.863e^-5	0.985	INTRON CG32432
2R	13443145	2R_13443145_SNP [dm3] 2R_17555640_SNP [dm6]	G	A	1.924e^-5	0.985	NON_SYNONYMOUS_CODING MESR4	TF binding site mE1_TFBS_cad mE1_TFBS_inv
2L	17653078	2L_17653078_SNP [dm3] 2L_17653078_SNP [dm6]	G	A	1.962e^-5	0.985	INTRON CadN
2R	13435278	2R_13435278_SNP [dm3] 2R_17547773_SNP [dm6]	C	T	2.128e^-5	0.985	START_GAINED MESR4 UTR_5_PRIME MESR4 UPSTREAM MESR4 & 1 other	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_twi BDTNP1_TFBS_z mE1_TFBS_cnc mE1_TFBS_D mE1_TFBS_h mE1_TFBS_HSA mE1_TFBS_jumu mE1_TFBS_kn mE1_TFBS_Trl mE1_TFBS_Ubx
X	7257488	X_7257488_SNP [dm3] X_7363455_SNP [dm6]	T	A	2.180e^-5	0.985	INTRON CG1677 & 1 other
2L	4061681	2L_4061681_SNP [dm3] 2L_4061681_SNP [dm6]	T	G	2.413e^-5	0.985	INTRON ed
2R	9190091	2R_9190091_SNP [dm3] 2R_13302586_SNP [dm6]	G	T	2.447e^-5	0.985	INTERGENIC
3L	9113407	3L_9113407_SNP [dm3] 3L_9120307_SNP [dm6]	A	T	2.473e^-5	0.985	INTRON bol
X	17125403	X_17125403_SNP [dm3] X_17231370_SNP [dm6]	A	C	2.500e^-5	0.985	UPSTREAM CG10597 INTERGENIC
2R	13436891	2R_13436891_SNP [dm3] 2R_17549386_SNP [dm6]	A	G	2.553e^-5	0.985	SYNONYMOUS_CODING MESR4	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_sens
2R	6375313	2R_6375313_SNP [dm3] 2R_10487808_SNP [dm6]	G	T	2.557e^-5	0.985	UTR_3_PRIME lola DOWNSTREAM lola INTRON lola	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi
2L	21952537	2L_21952537_SNP [dm3] 2L_21952537_SNP [dm6]	T	C	2.699e^-5	0.985	INTERGENIC
2R	10480943	2R_10480943_SNP [dm3] 2R_14593438_SNP [dm6]	T	C	2.708e^-5	0.985	SYNONYMOUS_CODING CG12869	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
2L	4399270	2L_4399270_SNP [dm3] 2L_4399270_SNP [dm6]	C	G	2.711e^-5	0.985	NON_SYNONYMOUS_CODING l_2_k05819
2L	18653594	2L_18653594_SNP [dm3] 2L_18653594_SNP [dm6]	C	A	2.746e^-5	0.985	UPSTREAM Cyp310a1 INTRON MESR3	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_HSA
X	15468685	X_15468685_SNP [dm3] X_15574652_SNP [dm6]	A	C	2.887e^-5	0.985	UPSTREAM CG9213 DOWNSTREAM CG42299 INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
2L	18482292	2L_18482292_SNP [dm3] 2L_18482292_SNP [dm6]	A	T	2.916e^-5	0.985	INTRON CG10283
2R	17837404	2R_17837404_SNP [dm3] 2R_21949899_SNP [dm6]	G	A	2.922e^-5	0.985	INTERGENIC
X	16639531	X_16639531_SNP [dm3] X_16745498_SNP [dm6]	G	T	2.937e^-5	0.985	INTRON CG9634
3L	1832610	3L_1832610_SNP [dm3] 3L_1832610_SNP [dm6]	G	A	2.992e^-5	0.985	UPSTREAM Cpr62Ba DOWNSTREAM Cpr62Bb INTERGENIC
2L	14001873	2L_14001873_SNP [dm3] 2L_14001873_SNP [dm6]	T	G	3.216e^-5	0.985	UPSTREAM rk INTERGENIC
3R	20842601	3R_20842601_SNP [dm3] 3R_25016879_SNP [dm6]	G	A	3.250e^-5	0.985	SYNONYMOUS_CODING tnc
2R	17095181	2R_17095181_SNP [dm3] 2R_21207676_SNP [dm6]	T	C	3.256e^-5	0.985	INTRON CG44245 & 1 other
X	16639520	X_16639520_SNP [dm3] X_16745487_SNP [dm6]	A	T	3.285e^-5	0.985	INTRON CG9634
2R	12302245	2R_12302245_SNP [dm3] 2R_16414740_SNP [dm6]	A	G	3.330e^-5	0.985	DOWNSTREAM Menl-2 & 1 other INTRON Sema-2b
X	19900547	X_19900547_INS [dm3] X_20006514_INS [dm6]	T	TT	3.364e^-5	0.985	UTR_3_PRIME Dop2R
X	15262101	X_15262101_DEL [dm3] X_15368068_DEL [dm6]	CCTCGGTCAGGCGCCCC...	C	3.517e^-5	0.985	INTRON acj6
2R	13432176	2R_13432176_DEL [dm3] 2R_17544671_DEL [dm6]	CGCGCCACC	C	3.572e^-5	0.985	UPSTREAM cyp33 DOWNSTREAM CG43370 INTRON CG34194	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_slp1 mE1_TFBS_HSA
2L	4062542	2L_4062542_SNP [dm3] 2L_4062542_SNP [dm6]	T	G	3.658e^-5	0.985	INTRON ed
3L	20876089	3L_20876089_SNP [dm3] 3L_20882989_SNP [dm6]	C	T	3.776e^-5	0.985	INTRON CG32432
2R	13444959	2R_13444959_SNP [dm3] 2R_17557454_SNP [dm6]	G	A	3.793e^-5	0.985	SYNONYMOUS_CODING Klp54D
X	1995606	X_1995606_INS [dm3] X_2101573_INS [dm6]	C	CC	3.804e^-5	0.985	UPSTREAM snoRNA:Me18S-C1024 & 1 other INTRON csw
2R	12302243	2R_12302243_SNP [dm3] 2R_16414738_SNP [dm6]	C	T	3.837e^-5	0.985	DOWNSTREAM Menl-2 & 1 other INTRON Sema-2b
3L	9952020	3L_9952020_SNP [dm3] 3L_9958920_SNP [dm6]	C	T	3.846e^-5	0.985	INTRON CG34356
2R	8782916	2R_8782916_SNP [dm3] 2R_12895411_SNP [dm6]	A	G	4.212e^-5	0.985	INTRON vg	regulatory region REDfly_CRMs TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi
2R	6568900	2R_6568900_SNP [dm3] 2R_10681395_SNP [dm6]	G	A	4.319e^-5	0.985	INTRON stan	TF binding site BDTNP1_TFBS_da mE1_TFBS_HSA
X	6882706	X_6882706_SNP [dm3] X_6988673_SNP [dm6]	C	A	4.349e^-5	0.985	INTRON ogre	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_gt BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_slp1 BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_D mE1_TFBS_HSA mE1_TFBS_Trl
X	6362486	X_6362486_SNP [dm3] X_6468453_SNP [dm6]	C	T	4.363e^-5	0.985	SYNONYMOUS_CODING CG42340	TF binding site mE1_TFBS_chinmo
3R	4030841	3R_4030841_SNP [dm3] 3R_8205119_SNP [dm6]	T	C	4.387e^-5	0.985	UPSTREAM CheA84a INTERGENIC	TF binding site BDTNP1_TFBS_bcd BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_gt BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_shn BDTNP1_TFBS_slp1 BDTNP1_TFBS_sna BDTNP1_TFBS_tll BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
2L	8889160	2L_8889160_SNP [dm3] 2L_8889160_SNP [dm6]	C	T	4.390e^-5	0.985	INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_bab1 mE1_TFBS_cad mE1_TFBS_GATAe mE1_TFBS_hkb mE1_TFBS_HSA mE1_TFBS_jumu mE1_TFBS_kn mE1_TFBS_sens mE1_TFBS_ttk
2L	15907859	2L_15907859_INS [dm3] 2L_15907859_INS [dm6]	A	TTTTTTTTTGCT...	4.651e^-5	0.985	INTRON beat-Ib
X	15550283	X_15550283_SNP [dm3] X_15656250_SNP [dm6]	G	A	4.681e^-5	0.985	INTERGENIC
2L	7755850	2L_7755850_DEL [dm3] 2L_7755850_DEL [dm6]	CGAGGGC	C	4.687e^-5	0.985	UPSTREAM CG14538 INTRON CG7196
X	6168949	X_6168949_SNP [dm3] X_6274916_SNP [dm6]	A	G	4.983e^-5	0.985	UTR_3_PRIME Spt6 DOWNSTREAM CG3566 & 1 other
2L	6177989	2L_6177989_SNP [dm3] 2L_6177989_SNP [dm6]	T	G	5.013e^-5	0.985	INTERGENIC	silencer mE1_HDAC_PRE TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_Trl
2L	2515087	2L_2515087_SNP [dm3] 2L_2515087_SNP [dm6]	G	T	5.014e^-5	0.985	INTERGENIC
2R	13436094	2R_13436094_DEL [dm3] 2R_17548589_DEL [dm6]	AT	A	5.063e^-5	0.985	INTRON MESR4	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_twi BDTNP1_TFBS_z mE1_TFBS_D mE1_TFBS_HSA mE1_TFBS_Trl
2R	13445298	2R_13445298_SNP [dm3] 2R_17557793_SNP [dm6]	A	T	5.122e^-5	0.985	INTRON Klp54D
X	12868567	X_12868567_DEL [dm3] X_12974534_DEL [dm6]	TT	T	5.178e^-5	0.985	DOWNSTREAM CG12716 & 1 other EXON CR43152
2R	19317162	2R_19317162_SNP [dm3] 2R_23429639_SNP [dm6]	A	G	5.189e^-5	0.985	INTRON CG9815
3L	3002787	3L_3002787_SNP [dm3] 3L_3002787_SNP [dm6]	C	T	5.423e^-5	0.985	UPSTREAM FMRFaR INTRON FMRFaR
2R	9179945	2R_9179945_SNP [dm3] 2R_13292440_SNP [dm6]	A	T	5.425e^-5	0.985	INTRON Dh31-R
X	15550239	X_15550239_SNP [dm3] X_15656206_SNP [dm6]	G	T	5.543e^-5	0.985	INTERGENIC
2R	13432572	2R_13432572_SNP [dm3] 2R_17545067_SNP [dm6]	G	T	5.619e^-5	0.985	UPSTREAM cyp33 DOWNSTREAM CG43370 & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_slp1 mE1_TFBS_D mE1_TFBS_h mE1_TFBS_HSA mE1_TFBS_jumu
X	16639257	X_16639257_SNP [dm3] X_16745224_SNP [dm6]	A	G	5.631e^-5	0.985	DOWNSTREAM Twdlalpha INTRON CG9634	TF binding site mE1_TFBS_HSA
2L	17457918	2L_17457918_SNP [dm3] 2L_17457918_SNP [dm6]	T	A	5.663e^-5	0.985	NON_SYNONYMOUS_CODING CG18563 INTRON CG5050
2L	16968287	2L_16968287_DEL [dm3] 2L_16968287_DEL [dm6]	GTTCAATGAGACAACCATTT...	G	5.700e^-5	0.985	INTERGENIC
2R	13157081	2R_13157081_SNP [dm3] 2R_17269576_SNP [dm6]	G	C	5.711e^-5	0.985	INTRON mbl	TF binding site mE1_TFBS_run
2R	7824515	2R_7824515_SNP [dm3] 2R_11937010_SNP [dm6]	C	T	5.736e^-5	0.985	INTERGENIC
2L	17544905	2L_17544905_SNP [dm3] 2L_17544905_SNP [dm6]	T	C	5.782e^-5	0.985	INTERGENIC
X	8714016	X_8714016_SNP [dm3] X_8819983_SNP [dm6]	T	C	5.788e^-5	0.985	INTERGENIC	TF binding site BDTNP1_TFBS_twi mE1_TFBS_HSA
2R	9971639	2R_9971639_SNP [dm3] 2R_14084134_SNP [dm6]	C	G	5.881e^-5	0.985	INTRON Prosap
2L	15000579	2L_15000579_SNP [dm3] 2L_15000579_SNP [dm6]	G	A	6.001e^-5	0.985	INTERGENIC
3R	15373339	3R_15373339_SNP [dm3] 3R_19547617_SNP [dm6]	C	T	6.130e^-5	0.985	INTRON Dys
X	18427433	X_18427433_SNP [dm3] X_18533400_SNP [dm6]	A	T	6.188e^-5	0.985	INTRON Bx	TF binding site BDTNP1_TFBS_dl
2L	17715881	2L_17715881_SNP [dm3] 2L_17715881_SNP [dm6]	G	T	6.209e^-5	0.985	SYNONYMOUS_CODING CadN INTRON CadN	TF binding site mE1_TFBS_bab1 mE1_TFBS_HSA mE1_TFBS_inv mE1_TFBS_sens
X	19969716	X_19969716_SNP [dm3] X_20075683_SNP [dm6]	T	C	6.214e^-5	0.985	INTERGENIC
X	12094259	X_12094259_SNP [dm3] X_12200226_SNP [dm6]	A	G	6.233e^-5	0.985	INTRON Ten-a
3L	2404684	3L_2404684_SNP [dm3] 3L_2404684_SNP [dm6]	G	A	6.320e^-5	0.985	SYNONYMOUS_CODING CG45186 INTRON CG45186	TF binding site mE1_TFBS_chinmo mE1_TFBS_sens
3L	17165728	3L_17165728_SNP [dm3] 3L_17172628_SNP [dm6]	C	A	6.340e^-5	0.985	INTRON Rbp6
2R	6894922	2R_6894922_SNP [dm3] 2R_11007417_SNP [dm6]	T	G	6.392e^-5	0.985	INTRON luna
2R	13387101	2R_13387101_DEL [dm3] 2R_17499596_DEL [dm6]	TGGCAGCA	T	6.427e^-5	0.985	INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_HSA
3R	26869336	3R_26869336_SNP [dm3] 3R_31043614_SNP [dm6]	T	C	6.430e^-5	0.985	DOWNSTREAM CG33920 INTRON CanA1
2L	9937742	2L_9937742_SNP [dm3] 2L_9937742_SNP [dm6]	G	A	6.500e^-5	0.985	SYNONYMOUS_CODING CG31712 DOWNSTREAM Apf EXON CR45007	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_sens
2R	17553016	2R_17553016_SNP [dm3] 2R_21665511_SNP [dm6]	A	T	6.560e^-5	0.985	NON_SYNONYMOUS_CODING CG42363 UTR_3_PRIME CG42362 UPSTREAM CG42364
2L	17457895	2L_17457895_SNP [dm3] 2L_17457895_SNP [dm6]	T	A	6.582e^-5	0.985	NON_SYNONYMOUS_CODING CG18563 INTRON CG5050

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By genomic position
Variant impact
Gene name

RPL32_CT phenotype

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results